This note covers the
following topics: Structural Biology and Amino acids, History of Macromolecular Crystallography, Amino acid Chirality,
Non-covalent interactions and Ramachandran Map, Secondary structures;
Introduction to Protein , Alpha-domain proteins I: Coiled coils and four-helix
bundle, ROP protein design, Alpha-domain proteins II: Large alpha-helical domain
and globin fold, Alpha or Beta-domain proteins, Beta-domain proteins.
This note explores the
concepts and algorithms that enable computational modeling of biological
molecules, in both theory and practice. Topics covered includes: The basics of
protein structure, Rosetta and structural modeling, Optimization techniques,
Analysis of protein structures and assessment of model quality, Full atom
refinement and side chain modeling, Hands-on: Side chain modeling, Homology
modelin, Protein-protein docking.
This note aims
to provide the knowledge of the basic protein molecular architecture and then to
connect it to the basic cellular processes like enzymatic activity, transport
and membrane functions.
These are notes about
using mathematics to study the molecular structure of molecules, especially long
organic molecules like DNA and proteins. Topics covered includes: Molecular
Genetics: DNA, Proteins, Frames and moving frames, Orthogonal transformations
and Rotations, Torsion angles and pdb files, X-ray Crystallography, Lattices,
and Fourier Series, Nuclear Magnetic Resonance and distance geometry, Protein
Folding.
This note explains the following topics: Taxonomy : Primary and Secondary
Structure, Motifs and Supersecondary Structure, Tertiary Structure and Fold
Types, Forces that Determine Protein Structure, Mechanisms of Protein Folding,
Multiscale Modeling of Electrostatics.